OMERO.figure

Current Version: 3.2.1

Fast figures from your OMERO images

Smart figures with metadata

OMERO is a server platform for managing biological images. See the
Open Microscopy Site for more info.
OMERO.figure combines OMERO's powerful image rendering and metadata to provide a
tool for rapid figure creation. Each panel of the figure becomes a multi-dimensional
image viewer, allowing you to zoom and pan, adjust rendering settings and even
scroll through Z and Time.
Figures can be exported as TIFF images or PDF documents, so you can move seamlessly to
other editing tools such as Adobe Illustrator.

Shortcuts for common tasks

Many tasks of figure creation are very time consuming when done manually.
OMERO.figure provides tools to get the job done quickly. All of these features
work with multiple selected panels at once, making it easy to keep similar
panels in sync.

Export with panel images: Optionally export all panels as separate TIFFs to validate figure building steps or for use elsewhere.

Power of the web

You can create beautiful figures in your browser, then share them with others.
Depending on your OMERO permissions settings, you can even make them public,
so everyone can explore your figures interactively.

Try it now!

We have created a live demo with several examples, based on figures published in the Journal of Cell Biology.
This is a 'static' demo app (not hosted on an OMERO server), so you can't save changes. All the image data
comes from the OMERO-powered JCB-DataViewer, where you can also browse the raw data.
Click figures for demos:

Warning:
OMERO.figure version 2.x requires OMERO.web 5.2.6 or newer. This is due to a Django Framework compatibility and to a required package reorganization in OMERO.figure in version 2.0 so the application can be distributed from Python Package Index PyPI.

Enabling figure export

This section assumes that an OMERO.server is already installed.
Figures can be exported as PDF or TIFF files using a script that runs on the OMERO.server. This script needs to be uploaded to the OMERO.server and its dependencies installed on the OMERO.server machine.
The script can be uploaded using two alternative workflows, both of which require you to be an admin.

Option 1: Connect to the OMERO server and upload script via the CLI. It is important to be in the correct directory when uploading so that the script is uploaded with the full path omero/figure_scripts/Figure_To_Pdf.py:
$ cd omero_figure/scripts
$ path/to/OMERO.server/bin/omero script upload omero/figure_scripts/Figure_To_Pdf.py --official

Option 2: Alternatively, before starting the OMERO.server, copy the script from the figure install /omero_figure/scripts/omero/figure_scripts/Figure_To_Pdf.py to the OMERO.server path/to/OMERO.server/lib/scripts/omero/figure_scripts. Then restart the OMERO.server.

Optional: Figure legends can be formatted using Markdown syntax. To see this correctly in the exported PDF info page, we need Python-markdown. For example, install on CentOS 7:
$ yum install python-markdown

Update instructions

Upgrade the app

Stop OMERO.web.
To upgrade from a version of OMERO.figure prior to 2.0.1:

Remove the 'figure' directory from within the directory that is on your PYTHONPATH.

If upgrading from OMERO.figure 1.0.0, you can update the
webclient link to figure,
so that it automatically opens the figure app in a new tab. Simply remove the old link and add back the
new one...
# In case you need to list current links...
$ bin/omero config get omero.web.ui.top_links
# Remove the figure link...
$ bin/omero config remove omero.web.ui.top_links '["Figure", "figure_index"]'
# Add back new link as described in the install instructions above